RetrogeneDB ID: retro_taes_53

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_2AL_scaff_6432447:2905..4540(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_2AL_115DFA3B8
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_4AL_4A747B462
• Aliases: None
• Description: None

Sequence

>retro_taes_53
ATGTCACCGATCTCGCTGGTTGGCCCGACGCCGGCCGACCACGAGAGCTCCGGCCGGTTAGAGAATCTTCTCCGTGAGGC
CGGCCTGTACGAGACCTCCGATGAGCTGGCGGTCCGCGAGGAGGTGCTGCGCGATCTCCAAGCCATCGTCGACCGGTGGG
TGAAGCGCGTCACCGCTCAGCGAGGGTTTCCCCACGGCATGGCTGAGCAGGCCACCGCCCTTCTGATTCCCTTCGGTTCG
TACCGTCTCGGCGTTCACGGCCGCGGCTCCGACATCGACGCCCTCGTCGTCGGCCCCTCCTACATCGACCGCGACCGCGA
CTTCTTCGCCGTGCTTGGCGGCGTGCTGGCGGAGACGGAGGCCGTGACGGAGCTGCAGCCTGTGCCTCGCGCGCACGTGC
CCGTCATCAAGATGAGCTTCCGCGGCGTGCAGGTGGACCTCCTCTACGCCGGCGTGTGCCTGCCCGTGGTGCCCAGGGAC
CTCGACCTGCGCGACCGCTCCGTTTTCCGCGGCATGGACCTGGCCTCCGCGCGCAGCCTCAACGGCGTGCGCGTCGCCGA
CGAGCTCCTGCGTCTCGTCCCGGACGCCGGCGCCTTCCGCACGACGCTGCGGTGCATCAAGCACTGGGCCAAGGCGCGGG
GCGTCTACTCCAACGTGATGGGGTTCCTCGGCGGCGTGGGCTGGGCGATCCTGGTGGCGCGCGTGTGCCAGCTCTACCCC
AACGCCGCGCCGAGCATGCTGGTGCCGCGCTTCTTCAAGATCTTCGCGCAGTGGAAGTGGCCCAACCCGGTGCTGCTGCG
GGACATCGAGCACGACGACGGCGGCGAGCTCGCGCTCCGGCTGCCCGTCTGGGACCCGCGGCGGAACCCGCGCGACAAGA
GCCACATCATGCCCGTCATCACGCCGGCCTACCCATGCATGAACTCGTGCTACAACGTCTCGCACCCCACCCTGCGGACC
ATCACGGAGCAGCTCCAGATCGGCAACGGCATCTGCCAGGAGATCCTCAAGGGCGGCGGCGCCGGCGGGTGGGACGCGCT
GTTCCAGCCGTTCCAGTTCTTCAAGGCGTACAAGAGCTACCTGCAGGTGGACGTGAAGGTCGCCGGAGGGGAGGCCGACC
TCCGGGAGTGGAAGGGGTGGGTGGAGTCGCGGCTGAGGCAGCTGGTGAACAGGGTCGAGATGGCCACGGCAAGCATGCTG
CTCTGCCATCCCAACCCGAAAGCCTACGCCGCCAAACCCCATGATCTCCACTGCACGTCAACCTTCTTCGTGGGCTTGTC
CAAGCCACAGCAGCAGCAGCAGCCCCAGGTGCCGTTCGACCTACGCGTGACGACGGAGGGGTTCAAGCAGGAGGTGTACA
CGTACGAGTTCTGGAGGCCCGGGATGGAGCTGGAGGTCTCGCACACCCGGAGGAGGGACCTGCCGTCCTACGTGCTCGAG
CAGATCCTCCCGGCTGGGCATCTCAAGAGGAAGCGCGTCGCCGAGAACAACTCTTCTCCTCCGTTGTCGTCTGCTTCCGG
CGAGGTCAAGAAGGTGGCGGCGGCCGGCGGAACCGGATCGGCGCCTGAGAGGAAGAGGCAATGCTGTCCCAGCAGCAACA
TCCTTCCCAGCGCTTCAGTACAGGGCGTTGTGTGA

Alignment

ORF - retro_taes_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.57 %
• Parental protein coverage: 64.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PISLGGPTEKDVVQTAEVEKFLADAGLYESQEEAVSREEVLGKLDQTVKTWIKKATRVSGYGEQFVQEAN
          PISL.GPT..D.......E..L..AGLYE...E...REEVL..L...V..W.K..T...G........A.
Retrocopy PISLVGPTPADHESSGRLENLLREAGLYETSDELAVREEVLRDLQAIVDRWVKRVTAQRGFPHGMAEQAT

Parental  AKIFTFGSYRLGVHGPGADIDTLCVGPRHATRNDYFFRCLHDMLAEMPEVSELHPVPDAHVPVLGFKLCG
          A....FGSYRLGVHG.G.DID.L.VGP....R...FF..L...LAE...V.EL.PVP.AHVPV......G
Retrocopy ALLIPFGSYRLGVHGRGSDIDALVVGPSYIDRDRDFFAVLGGVLAETEAVTELQPVPRAHVPVIKMSFRG

Parental  VSIDLLYANLAHVVIPDDLDLSQDSILHNVDEQAVRSLNGCRVTDQILRLVPNIPSFRTTLRFMRYWGKR
          V..DLLYA.....V.P.DLDL...S.....D....RSLNG.RV.D..LRLVP....FRTTLR....W.K.
Retrocopy VQVDLLYAGVCLPVVPRDLDLRDRSVFRGMDLASARSLNGVRVADELLRLVPDAGAFRTTLRCIKHWAKA

Parental  RGVYSNVMGFLGGINWAILVARICQLYPNASPSMLISRFFRVYSQWKWPNPVTLCHIEE---GPLGL--P
          RGVYSNVMGFLGG..WAILVAR.CQLYPNA.PSML..RFF....QWKWPNPV.L..IE....G.L.L..P
Retrocopy RGVYSNVMGFLGGVGWAILVARVCQLYPNAAPSMLVPRFFKIFAQWKWPNPVLLRDIEHDDGGELALRLP

Parental  VWDPRRNFRDRGHQMPIITPAYPCMNSSYNVSTSTRYVMVQEFTRGYEICQAIDENRAT--WDDLFEPYP
          VWDPRRN.RD..H.MP.ITPAYPCMNS.YNVS..T..........G..ICQ.I........WD.LF.P..
Retrocopy VWDPRRNPRDKSHIMPVITPAYPCMNSCYNVSHPTLRTITEQLQIGNGICQEILKGGGAGGWDALFQPFQ

Parental  FFELYKNYLEVGI-TARNEDDLRNWKGWVESRLRTLVLKFERYTHEMLLAHPHPRDFSDGSRPLH--SFY
          FF..YK.YL.V....A..E.DLR.WKGWVESRLR.LV...E..T..MLL.HP.P.........LH..S..
Retrocopy FFKAYKSYLQVDVKVAGGEADLREWKGWVESRLRQLVNRVEMATASMLLCHPNPKAYAAKPHDLHCTSTF

Parental  FMGLWRKQTAQPQEAEQFDIRGIVNEFKSAVLAYAHRREGMDIEVSHVKRKDIPLFV
          F.GL...Q..Q.Q....FD.R.....FK..V..Y...R.GM..EVSH..R.D.P..V
Retrocopy FVGLSKPQ-QQQQPQVPFDLRVTTEGFKQEVYTYEFWRPGMELEVSHTRRRDLPSYV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Triticum aestivum was not studied using RNA-Seq expression data.

ChIP-Seq

Triticum aestivum was not studied using ChIP-Seq data.

EST

Triticum aestivum was not studied using EST data.

TSS

Triticum aestivum was not studied using FANTOM5 data.

Lab

retro_taes_53 was not experimentally validated.

Homology

Retrocopy orthology:

Triticum aestivum does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo8g104580	1 retrocopy	retro_bole_26,
Brassica rapa	Bra031010	1 retrocopy	retro_brap_15,
Triticum aestivum	Traes_4AL_4A747B462	1 retrocopy	retro_taes_53 ,